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Crystal structure of frog M-ferritin E130A_M161E mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 2.0 M MgCl2 and 100 mM Bicine (pH 9.0)
Crystal Properties Matthews coefficient Solvent content 3.28 61.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.032 α = 90 b = 184.032 β = 90 c = 184.032 γ = 90
Symmetry Space Group F 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 CCD MARMOSAIC 225 mm CCD 2015-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9794 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.5 41.19 100 1 27.3 14.2 43133
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.963
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3KA3 1.5 41.19 40992 2141 99.9 0.128 0.1442 0.163 0.1765 RANDOM 13.05
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.339 r_scangle_it 8.639 r_scangle_other 8.635 r_scbond_other 6.754 r_scbond_it 6.537 r_mcangle_other 4.951 r_dihedral_angle_1_deg 4.922 r_mcangle_it 4.842 r_mcbond_other 4.067 r_mcbond_it 3.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.339 r_scangle_it 8.639 r_scangle_other 8.635 r_scbond_other 6.754 r_scbond_it 6.537 r_mcangle_other 4.951 r_dihedral_angle_1_deg 4.922 r_mcangle_it 4.842 r_mcbond_other 4.067 r_mcbond_it 3.745 r_rigid_bond_restr 3.63 r_angle_refined_deg 1.984 r_angle_other_deg 0.809 r_nbd_other 0.281 r_xyhbond_nbd_refined 0.254 r_nbd_refined 0.246 r_nbtor_refined 0.189 r_chiral_restr 0.137 r_metal_ion_refined 0.134 r_symmetry_metal_ion_refined 0.107 r_xyhbond_nbd_other 0.022 r_gen_planes_other 0.02 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_other r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1430 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction Aimless data scaling MOLREP phasing